[Effect of electroacupuncture on visceral sensitivity and colonic NGF, TrkA, TRPV1 expression in IBS-D rats].

OBJECTIVE: To observe the effect of electroacupuncture (EA) at "Tianshu" (ST 25) and "Shangjuxu" (ST 37) on mental state, visceral sensitivity and protein expression of nerve growth factor (NGF), tyrosine kinase receptor A (TrkA) and transient receptor potential vanilloid 1 (TRPV1) of colonic tissue in diarrhea-predominant irritable bowel syndrome (IBS-D) rats, and to explore its possible mechanism on treating IBS-D. METHODS: A total of 36 male SD rats of SPF grade were randomized into a blank group, a model group, an EA group and a western medication group, 9 rats in each group. In the model group, the EA group and the western medication group, IBS-D model was established by enema of dinitrobenzene sulfonic acid (DNBS) combined with chronic restraint stress method. In the EA group, EA was applied at "Tianshu" (ST 25) and "Shangjuxu" (ST 37), with disperse-dense wave, in frequency of 2 Hz/100 Hz, 20 min each time, once a day for 7 days. In the western medication group, pinaverium bromide suspension was given by gavage (15 mg•kg-1•d-1) for 7 days. Before and after model establishment, and after intervention, the body mass, 24 h food intake and fecal water content were observed, the visceral sensitivity was detected by abdominal withdrawal reflex (AWR); after intervention, the mental state was evaluated by elevated plus maze (EPM) test, the protein expression of NGF, TrkA and TRPV1 was detected by immunohistochemistry and Western blot in the 4 groups. RESULTS: After model establishment, compared with the blank group, the body mass and 24 h food intake were decreased (P<0.05), first systolic latency of AWR was shortened and number of contraction wave of AWR was increased (P<0.05), and fecal water content was increased (P<0.05) in the model group, the EA group and the western medication group. After intervention, compared with the blank group, open arm residence time ratio (OT%) of EPM was decreased (P<0.05) and protein expression of NGF, TrkA, TRPV1 in colonic tissue was increased in the model group (P<0.05); compared with the model group, the body mass and 24 h food intake were increased (P<0.05), first systolic latency of AWR was lengthened and number of contraction wave of AWR was decreased (P<0.05), the fecal water content was decreased (P<0.05), OT% of EPM was increased (P<0.05), and protein expression of NGF, TrkA, TRPV1 in colonic tissue was decreased (P<0.05) in the EA group and the western medication group. CONCLUSION: Electroacupuncture at "Tianshu" (ST 25) and "Shangjuxu" (ST 37) can relieve the anxiety and depression-like behaviors in IBS-D rats, down-regulate the protein expression of NGF, TrkA, TRPV1 in colonic tissue, so as to reduce the visceral sensitivity and relieve symptoms.

[MA Hui-fang's experience in age-related macular degeneration treated with acupuncture at Jingming (BL 1)].

The paper introduces professor MA Hui-fang's experience in age-related macular degeneration treated with acupuncture at Jingming (BL 1). It is believed that the basic pathogenesis of this disease refers to liver and kidney insufficiency and weakness of spleen qi. Based on the academic ideas of yang qi and meridian-collateral system, the treatment principle is proposed as "invigorating yang qi, replenishing the liver and kidney and nourishing the spleen and stomach". Regarding acupoint selection, Jingming (BL 1) is specially used, combined with the 4 front-mu points (Zhongwan [CV 12], Guanyuan [CV 4] and bilateral Tianshu [ST 25]), as well as the empirical points for eye diseases (Jingming [BL 1], Baihui [GV 20] and Zulinqi [GB 41]). Concerning to needling technique, shuci (transport needling), fenci (intermuscular needling) and yuandaoci (distal needling) are dominated. Eventually, a set of unique therapeutic method has been accumulated through professor MA Hui-fang's clinical practice in treatment of age-related macular degeneration.

A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization.

MOTIVATION: With the great progress of deep learning-based inter-residue contact/distance prediction, the discrete space formed by fragment assembly cannot satisfy the distance constraint well. Thus, the optimal solution of the continuous space may not be achieved. Designing an effective closed-loop continuous dihedral angle optimization strategy that complements the discrete fragment assembly is crucial to improve the performance of the distance-assisted fragment assembly method. RESULTS: In this article, we proposed a de novo protein structure prediction method called IPTDFold based on closed-loop iterative partition sampling, topology adjustment and residue-level distance deviation optimization. First, local dihedral angle crossover and mutation operators are designed to explore the conformational space extensively and achieve information exchange between the conformations in the population. Then, the dihedral angle rotation model of loop region with partial inter-residue distance constraints is constructed, and the rotation angle satisfying the constraints is obtained by differential evolution algorithm, so as to adjust the spatial position relationship between the secondary structures. Finally, the residue distance deviation is evaluated according to the difference between the conformation and the predicted distance, and the dihedral angle of the residue is optimized with biased probability. The final model is generated by iterating the above three steps. IPTDFold is tested on 462 benchmark proteins, 24 FM targets of CASP13 and 20 FM targets of CASP14. Results show that IPTDFold is significantly superior to the distance-assisted fragment assembly method Rosetta_D (Rosetta with distance). In particular, the prediction accuracy of IPTDFold does not decrease as the length of the protein increases. When using the same FastRelax protocol, the prediction accuracy of IPTDFold is significantly superior to that of trRosetta without orientation constraints, and is equivalent to that of the full version of trRosetta. AVAILABILITYAND IMPLEMENTATION: The source code and executable are freely available at https://github.com/iobio-zjut/IPTDFold. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

[Effect of acupuncture on intestinal flora and TLR4 in brain and intestinal tissues in rats with stress gastric ulcer].

OBJECTIVE: To observe the effect of acupuncture at "Guanyuan" (CV 4) and "Xiajuxu" (ST 39) on intestinal flora and Toll-like receptors-4 (TLR4) in brain and intestinal tissue in rats with stress gastric ulcer (SGU), and to explore the possible mechanism of acupuncture for SGU. METHODS: Thirty-one male SD rats were randomly divided into a blank group (n=7), a model group (n=8), an acupuncture group (n=8) and a drug group (n=8). The rats in the model group, acupuncture group and drug group were treated with modified restraint plus water-immersion stress method to establish SGU model. After modeling, the rats in the acupuncture group were treated with acupuncture at "Guanyuan" (CV 4) and "Xiajuxu" (ST 39), 20 min each time, and the needles were twirled for 30 s every 5 min. The rats in the drug group were treated with intragastric administration of 2 mL omeprazole enteric-coated tablets (20 mg/mL). Both the treatments were given once a day for 5 days. After the intervention, the gastric mucosal damage index was calculated by Guth method; the morphological changes of gastric mucosa were observed by HE staining; the diversity of intestinal flora was detected by 16S rDNA high-throughput sequencing; TLR4 contents in brain and intestinal tissues were determined by ELISA. RESULTS: Compared with the blank group, the gastric mucosal damage index was significantly increased in the model group (P<0.01); the morphological changes of gastric mucosa were obvious; the Observed Species index and Shannon index of α diversity index of intestinal flora were decreased (P<0.05); the ß diversity showed that the spatial distance between the model group and the blank group was far; the TLR4 contents in the brain and intestinal tissue were increased (P<0.05, P<0.01). Compared with the model group, the gastric mucosal damage index was decreased in the acupuncture group and the drug group (P<0.05); the morphology of gastric mucosa was improved; the Observed Species index and Shannon index of α diversity index of intestinal flora in the acupuncture group was increased (P<0.05), and the Shannon index in the drug group was increased (P<0.05); the ß diversity showed that the spatial distance between the acupuncture group and the blank group was close; the TLR4 contents in the brain and intestinal tissues of the acupuncture group were decreased (P<0.01). Compared with the drug group, the contents of TLR4 in the intestinal tissue of the acupuncture group were decreased (P<0.05). CONCLUSION: Acupuncture at "Guanyuan" (CV 4) and "Xiajuxu" (ST 39) could alleviate SGU in rats, and its mechanism may be related to increasing the diversity of intestinal flora, promoting the disorder of intestinal flora to normal, and reducing the overexpression of TLR4 in brain and intestinal tissues.

Protein Structure Prediction Using Population-Based Algorithm Guided by Information Entropy.

Ab initio protein structure prediction is one of the most challenging problems in computational biology. Multistage algorithms are widely used in ab initio protein structure prediction. The different computational costs of a multistage algorithm for different proteins are important to be considered. In this study, a population-based algorithm guided by information entropy (PAIE), which includes exploration and exploitation stages, is proposed for protein structure prediction. In PAIE, an entropy-based stage switch strategy is designed to switch from the exploration stage to the exploitation stage. Torsion angle statistical information is also deduced from the first stage and employed to enhance the exploitation in the second stage. Results indicate that an improvement in the performance of protein structure prediction in a benchmark of 30 proteins and 17 other free modeling targets in CASP.

[Overview of systematic review on acupoint application for bronchial asthma].

OBJECTIVE: To overview the systematic review/meta-analysis on acupoint application for bronchial asthma. METHODS: A computerized retrieval was performed from 6 databases, named CNKI, CBM, VIP, WF, PubMed and Cochrane Library. The time of retrieval was from the establishment of the database to April 1, 2019. According to the inclusion and exclusion criteria, the two researchers independently selected articles and extracted data. In case of disagreement, a third party was adopted to solve it. Using AMSTAR2, PRISMA and GRADE, the literature quality and evidence grade were assessed. RESULTS: A total of 19 articles relevant with systematic evaluation/meta-analysis were included, 16 articles of which were in Chinese and 3 articles in English, published in the period from 2007 to 2018. Forty-two outcome indicators were included. It was found that the quality of methodology was very low, the quality of literature report has some or serious flaws and the quality level of evidence is mostly low or very low. CONCLUSION: Currently, regarding the articles of systematic review/meta-analysis on acupoint application for bronchial asthma, it is quite low in methodological quality and literature report quality and is not high in the grade of outcome indicators. The clinical research should be intensively specified in association with the characteristics of traditional Chinese medicine so as to provide more reliable clinical evidence.

[Effect of acupuncture on serum inflammatory cytokines and intestinal flora in rats with stress-induced gastric ulcer].

OBJECTIVE: To investigate the effect of acupuncture on serum inflammatory cytokines and intestinal flora in rats with stress-induced gastric ulcer (SGU), and to explore the mechanism of acupuncture in the treatment of SGU. METHODS: Sprague-Dawley rats were randomly divided into blank, model, acupuncture, and medication groups, with 7 rats in each group. Restraint water-immersion stress was used to establish the model of SGU. The rats in the acupuncture group were given acupuncture at "Zhongwan"(CV12) and bilateral "Zusanli"(ST36) for 20 min, once a day for 5 days, and those in the medication group were given 2 mL solution of Omeprazole enteric-coated tablets (0.2 mg/kg) by gavage, once a day for 5 days. The Guth method was used to calculate the gastric mucosa damage index, HE staining was used to observe the histopathological changes of the gastric mucosa, ELISA was used to measure the serum levels of interleukin-4 (IL-4) and interleukin-6 (IL-6), and 16S rDNA sequencing method was used to observe the change in intestinal flora. RESULTS: Compared with the blank group, the model group had a significant increase in gastric mucosa damage index (P<0.01), markedly pathological changes of the gastric mucosa shown by HE staining, a significant reduction in the content of serum IL-4 (P<0.01), and a significant increase in the content of serum IL-6 (P<0.01), as well as a significant reduction in Bacteroidetes and Firmicutes at the phylum level. Compared with the model group, the acupuncture group and the medication group had a significant reduction in gastric mucosa damage index (P<0.01, P<0.05). HE staining showed reduced pathological changes of the gastric mucosa, as well as a significant increase in the content of serum IL-4 (P<0.01, P<0.05) and a significant reduction in the content of serum IL-6 (P<0.01, P<0.05). As for the intestinal flora, there was a significant increase in Bacteroidetes. Compared with the medication group, the gastric mucosa damage index was decreased （P<0.05），the content of serum IL-4 was significantly increased （P<0.05）, while the content of serum IL-6 significantly decreased (P<0.05) in the acupuncture group. CONCLUSION: Acupuncture at CV12 and ST36 can down-regulate the content of serum IL-6, up-regulate the content of serum IL-4, maintain the relative homeostasis of inflammatory cytokines, and regulate the community structure of intestinal flora, and thus help to repair the damage of gastric mucosa.

[Effect of acupuncture on intestinal flora in rats with stress gastric ulcer].

OBJECTIVE: To observe the effect of acupuncture at "Baihui" (GV 20), "Zhongwan" (CV 12) and "Zusanli" (ST 36) on intestinal flora in rats with stress gastric ulcer (SGU) , and to explore the mechanism of acupuncture promoting SGU recovery. METHODS: Thirty-one SPF SD rats were randomly divided into a control group (7 rats), a model control group (8 rats), an acupuncture group (8 rats) and a medication group (8 rats). The rats in the model group, acupuncture group and medication group were selected to applied the improved restraint water-immersion stress method to establish the SGU model. After modeling, the rats in the control group and model group were fixed and restrained for 20 min every day for a total of 5 days; the rats in the acupuncture group were intervented with acupuncture at "Baihui" (GV 20), "Zhongwan" (CV 12) and "Zusanli" (ST 36), once a day, 20 min each time, and twisting needle for 30 s every 5 min for a total of 5 days; the rats in the medication group were gavaged by solution of omeprazole enteric-coated tablet (200 mg/mL), 2 mL for each rat, once a day. Guth method was used to calculate the gastric mucosal damage index (GMDI), HE staining was used to observe the pathological changes of gastric mucosa, and 16SrDNA identification was used to detect the structural abundance of intestinal flora. RESULTS: Compared with the control group, the GMDI of rats in the model group was increased (P<0.01), the gastric mucosal pathological changes were significant, and the intestinal flora richness index Chao1, Observed species and diversity index Shannon were all decreased (P<0.05), the diversity index Simpson was increased (P<0.05). Compared with the model group, the GMDI of rats in the acupuncture group and medication group was reduced (P<0.01, P<0.05), the gastric mucosal damage degree was reduced, and the intestinal flora richness index Chao1, Observed species and diversity index Shannon were all increased (P<0.05) and the diversity index Simpson decreased (P<0.05). Compared with the medication group, the GMDI of rats in the acupuncture group was reduced (P<0.01), the recovery of gastric mucosal injury was better than that of the medication group. CONCLUSION: Acupuncture can effectively improve gastric mucosal injury of SGU, and the mechanism may be related to increasing the diversity of intestinal flora and promoting the correction of the disordered intestinal flora.

Two-Stage Distance Feature-based Optimization Algorithm for De novo Protein Structure Prediction.

De novo protein structure prediction can be treated as a conformational space optimization problem under the guidance of an energy function. However, it is a challenge of how to design an accurate energy function which ensures low-energy conformations close to native structures. Fortunately, recent studies have shown that the accuracy of de novo protein structure prediction can be significantly improved by integrating the residue-residue distance information. In this paper, a two-stage distance feature-based optimization algorithm (TDFO) for de novo protein structure prediction is proposed within the framework of evolutionary algorithm. In TDFO, a similarity model is first designed by using feature information which is extracted from distance profiles by bisecting K-means algorithm. The similarity model-based selection strategy is then developed to guide conformation search, and thus improve the quality of the predicted models. Moreover, global and local mutation strategies are designed, and a state estimation strategy is also proposed to strike a trade-off between the exploration and exploitation of the search space. Experimental results of 35 benchmark proteins show that the proposed TDFO can improve prediction accuracy for a large portion of test proteins.

[Moxibustion improved gastric ulcer by reducing contents of corticotrophin-releasing hormone and adrenocorticotropic hormone in serum and hypothalamus-pituitary tissues in rats with stress-induced gastric ulcer].

OBJECTIVE: To observe the effect of moxibustion of "Zhongwan" (CV12) and "Zusanli" (ST36) on histopathological changes of the gastric mucosa and contents of corticotropin-releasing hormone(CRH) and adrenocorticotrophic hormone(ACTH) in the serum, hypothalamus and pituitary tissues in rats with stress-induced gastric ulcer(SGU), so as to reveal its mechanisms underlying improvement of SGU. METHODS: A total of 28 male SD rats were randomly divided into blank control, model, moxibustion, and medication groups, with 7 rats in each group. The SGU model was established by water immersion restraint stress for 3 h. Moxibustion was applied to "Zhongwan"(CV12) and bilateral "Zusanli" (ST36) for 20 min, once a day for 5 days, and rats of the medication group were treated by gavage of Omeprazole enteric-coated tablets (0.2 mg/kg) once a day for 5 days. The gastric mucosal damage index (ulcer index, UI) was measured to assess the injury severity according to Guth's me-thods. Histopathological changes of the gastric mucosa were determined by H．E. staining. The contents of CRH in serum and hypothalamus and ACTH in serum and pituitary gland tissue were assayed by using ELISA. RESULTS: Outcomes of H．E. staining showed gastric mucosal epithelia defect, disordered arrangement of glands, obvious mucosal hyperemia and edema, exudation of a large number of red blood cells, swelling of mucosal cells with necrosis of nuclei in the model group. These situations were relatively milder in the moxibustion and medication groups. After modeling, the UI, and the contents of CRH in the serum and hypotha-lamus, and ACTH in the serum and pituitary tissue were significantly increased in comparison with the blank control group (P<0.01). Following the intervention, the UI, and contents of CRH in the serum and hypothalamus, and ACTH in the serum and pituitary were all down-regulated in both medication and moxibustion groups relevant to the model group (P<0.05, P<0.01). The therapeutic effect of moxibustion was notably superior to that of medication in down-regulating serum CRH and ACTH (P<0.05). No significant differences were found between the medication and moxibustin interventions in lowering the UI, hypothalamic CRH and pituitary ACTH levels (P>0.05)．. CONCLUSION: Moxibustion can relieve gastric mucosal injury induced by stress in water immersion restraint stress rats, which may be associated with its effects in down-regulating the levels of CRH and ACTH in se-rum, hypothalamus and pituitary tissues (inhibition of activities of hypothalamic-pituitary-adrenocortical axis)．.